In the opening chapters (1 through 4), Meyer recounts that despite the hopes of many evolutionary biologists, the Cambrian explosion has proven to be a real event, not the artifact of an imperfect fossil record. Chapters 5 and 6 show how the lack of Precambrian ancestors to the Cambrian animals has not been resolved by studying genes, which instead accentuate the problem. Chapters 8 through 12 demonstrate that classical neo-Darwinian mechanisms have failed to explain the origin of new genetic information necessary to produce new proteins and animal forms. Chapters 13 and 14 further show that the neo-Darwinian mechanism cannot explain the epigenetic information and developmental processes required to evolve new body plans. Meyer then examines various “post-Darwinian” models of evolution, showing that they also fail to explain the origin of animal complexity (chapters 15 and 16).

In the final four chapters, Meyer identifies one post-Darwinian model that can explain the Cambrian explosion. Using standard scientific methods of historical sciences and rigorous abductive logic, Meyer establishes intelligent design as the only known cause capable of generating the information required to build the complex animals which appear explosively in the Cambrian.

What Did Darwin Say?“When Charles Darwin finished his famous book, he thought that he had explained every clue but one,”1 writes the Stephen C. Meyer, a Cambridge University trained philosopher of science, in the opening pages of Darwin’s Doubt. That “clue” was the sudden appearance of the major groups of animals (called “phyla”) in a geological layer millions of years old. At the time Darwin published Origin of Species, that section of rock was known as the Silurian period, but it was later renamed the Cambrian after an exposure of ancient rocks in Wales (classically called “Cambria”). Darwin explained that his theory required ancestors for these organisms:

If my theory be true, it is indisputable that before the lowest Silurian [Cambrian] stratum was deposited, long periods elapsed … and that during these vast, yet quite unknown, periods of time, the world swarmed with living creatures.2

But there was a problem. The fossil record did not supply these swarms of early ancestors to the complex animal forms that appear in the Cambrian—organisms as diverse as arthropods, mollusks, echinoderms, and, as we now know today, even vertebrate fish. Critics raised this problem, and in response Darwin pled no contest:

To the question why we do not find rich fossiliferous deposits belonging to these assumed earliest periods prior to the Cambrian system, I can give no satisfactory answer. … The case at present must remain inexplicable; and may be truly urged as a valid argument against the views here entertained.3

While Darwin’s theory of evolution has changed significantly since 1859, this unexplained piece of evidence—now called the Cambrian explosion—persists to the present day. Darwin’s Doubt explores what became of this enigma, and why it underscores a fundamental problem with unguided models of evolution. Meyer argues in Darwin’s Doubt that only the theory of intelligent design (ID) can explain the origin of the information required to build animal body plans. Indeed, Meyer’s book may be the most comprehensive critique of the neo-Darwinian paradigm written to date.

The first is the one we saw Darwin acknowledge in Origin of Species—namely that the geologically sudden appearance of many novel forms of animal life in the Cambrian period, and the absence of fossilized ancestral precursors for most of these animals in lower Precambrian strata, challenges the gradualistic picture of evolution envisioned by both Darwin and modern neo-Darwinists. To establish this point, Meyer must first rebut those who maintain the Cambrian “explosion” is an illusion.

Darwin’s preferred explanation for the lack of ancestral forms was the imperfection of the fossil record, which Stephen Jay Gould famously noted “still persists as the favored escape of most paleontologists from the embarrassment of a record that seems to show so little of evolution.”4 Thus many modern evolutionary biologists claim the Cambrian explosion never happened, and is merely an artifact of an imperfect record, because the evolutionary precursors to the Cambrian animals were simply too small or soft-bodied to have been fossilized.

Meyer answers this objection persuasively. Many Precambrian rocks should have been suitable for preserving fossils, and though they have been combed for over 150 years now, they still haven’t yielded evolutionary precursors to the Cambrian animals. This is not to say there are no fossils in Precambrian rock. In fact the Precambrian strata has yielded many fossils of organisms as small and soft-bodied as bacteria. As Meyer explains in chapter 3: “If paleontologists can find tiny fossilized cells in these far older and rarer formations, shouldn’t they also be able to find some ancestral forms of the Cambrian animals in younger and more abundant sedimentary rocks?”5

Other critics claim the Precambrian rock has in fact yielded the long-lost ancestors of the Cambrian animals. For example, prior to the Cambrian we find fossils of an enigmatic group of organisms called the Ediacaran fauna. However, as Meyer explains in chapter 4, most Cambrian paleobiologists doubt they were ancestral to the modern animal phyla. As the journal Nature recently noted, if the Ediacaran fauna “were animals, they bore little or no resemblance to any other creatures, either fossil or extant,”6 and therefore cannot be considered the missing ancestors.

Can the Genetic Evidence Save the Day?In light of this evidence, some evolutionary scientists maintain there is no need to find fossils establishing the ancient Precambrian evolution of the animal phyla, because genetic evidence demonstrates that this evolution took place. Meyer devotes two chapters to testing this approach.

In chapter 5, he evaluates the “molecular clock” hypothesis, which proposes that by using known mutation rates and comparing the differences between genes of living organisms, we can determine how long ago they shared a common ancestor. Molecular clock studies, however, are notoriously fraught with difficulties, and make dubious assumptions. One paper in Trends in Genetics compared molecular clock methods to “reading the entrails of chickens,”7 and another in Annual Review of Earth and Planetary Sciences admitted, “The idea that there is a universal molecular clock ticking away has long since been sdiscredited.”8

Such criticisms reflect the fact that molecular clock studies have yielded widely divergent dates for the supposed most recent common ancestors of animals. As Meyer documents, some molecular clock studies place the most recent common ancestor after the Cambrian explosion and others calculate that the common ancestors of various animal groups lived prior to the origin of the universe—obviously absurd results.9

But there’s a deeper assumption made by molecular clock studies that Meyer uncovers, namely that common ancestry of the animals is true. To be sure, intelligent design is not inherently incompatible with common ancestry, but Meyer points out that these studies “assume the existence of such ancestors, and then merely attempt, given that assumption, to determine how long ago such ancestors might have lived.”10 Should this assumption be granted?

In light of the failure of molecular clocks, some evolutionary biologists argue that even if we cannot determine exactly when animal groups diverged, we can still construct evolutionary “phylogenetic” trees to establish that they are in fact related. Here, again, Meyer documents how these efforts have failed.

In chapter 6, Meyer reviews attempts to construct a grand animal “tree of life.” The problem is, which tree is the correct one? As biologists have sequenced the genomes of more and more organisms, they have found that one gene yields one tree, and another gene will yield an entirely different, conflicting tree. In the same way, trees based upon anatomical characteristics often conflict with DNA-based trees. A 2012 paper in Biological Reviews of the Cambridge Philosophical Society observed that this sort of “phylogenetic conflict is common, and frequently the norm rather than the exception."11 One prominent study in the journal Science sought to construct an animal tree, and was forced to conclude that “Despite the amount of data and breadth of taxa analyzed, relationships among most metazoan phyla remained unresolved."12 A biologist quoted in New Scientist didn't put it so gently: “We’ve just annihilated the tree of life.”13

Like molecular clocks, attempts to construct a grand tree of life are also based upon assumptions, specifically that shared biological similarity is the result of inheritance from a common ancestor. But Meyer notes that a whole host of processes like convergent evolution and horizontal gene transfer cause that assumption to fail. As Meyer puts it, the logic used to generate evolutionary trees is reduced to “similarity implies common ancestry, except—we now learn—in those many, many cases when it does not.”14

In essence, attempts to establish the evolutionary relatedness and deep Precambrian history of the animal phyla have failed both in theory, and on the facts.

Leading Authorities AgreeHaving shown that the Cambrian explosion was a real event, we can appreciate the scale of novel animal diversity that it entails. After reviewing the paleontological literature, Meyer concludes that in the explosion, “representatives of about twenty of the roughly twenty-six total phyla present in the known fossil record made their first appearance.”15 Organisms with modern-looking eyes, legs, heads, tails, tentacles, pinchers, mouths, and guts—requiring untold numbers of new genes, cell types, tissues, and organs—burst onto the scene abruptly.

Two of the most prominent authorities in Cambrian paleobiology recently affirmedMeyer’s basic position about the scale of the explosion. In March of 2013, Douglas Erwin of the Smithsonian Institution’s National Museum of Natural History, and UC Berkeley professor James Valentine, co-published a comprehensive volume on the topic, The Cambrian Explosion: The Construction of Animal Biodiversity. In a “geologically brief interval between about 530 to 520 Ma,” Erwin and Valentine explain, “all or nearly all the major phylum-level groups of living animals, including many small softbodied groups that we do not actually find as fossils, had appeared by the end of the early Cambrian.”16

They note that while some maintain that “this geologically abrupt and spectacular record of early animal life” does not represent a real event in life’s history, the skeptics “have not diminished the magnitude or importance of the explosion.” Instead, “[s]everal lines of evidence are consistent with the reality of the Cambrian explosion.”17 Indeed, the consensus among Cambrian experts seems to have been expressed in a 2009 paper in BioEssays:

[A]s explained on an intelligent-design t-shirt.

Fact: Forty phyla of complex animals suddenly appear in the fossil record, no forerunners, no transitional forms leading to them; “a major mystery,” a “challenge.” The Theory of Evolution – exploded again (idofcourse.com).

Although we would dispute the numbers, and aside from the last line, there is not much here that we would disagree with. Indeed, many of Darwin's contemporaries shared these sentiments, and we assume—if Victorian fashion dictated—that they would have worn this same t-shirt with pride.18

Having affirmed that the explosion was real, the paper acknowledges that “elucidating the materialistic basis of the Cambrian explosion has become more elusive, not less, the more we know about the event itself.”19 But is it correct that “materialist” explanations have (as of yet, at least) failed to explain the Cambrian explosion?

Testing the Neo-Darwinian MechanismAfter establishing that the Cambrian explosion was a real event in the history of life, Meyer makes his second main challenge, arguing that the neo-Darwinian mechanism lacks the creative power to produce the new animal forms which first appear in the Cambrian. In particular, he argues that the mutation and natural selection mechanism cannot produce both the genetic and epigenetic information necessary to build the complex animal body plans that arise in Cambrian. Meyer offers five separate lines of evidence and arguments to support this latter claim:

Building off the first point, Meyer shows that multiple coordinated mutations are necessary to produce functional proteins, but these could not arise within realistic waiting times allowed by the fossil record.

Next Meyer shifts his attention to animal development, showing that the neo-Darwinian mechanism could not produce new body plans given that mutagenesis experiments show how early acting body plan mutations—the very mutations that would be necessary to produce whole new animals from a pre-existing animal body plan—inevitably produce embryonic lethals (i.e., dead organisms).

Meyer’s fourth critique of the neo-Darwinian mechanism explains why mutations could not alter developmental gene regulatory networks necessary to produce new ones, as producing such new regulatory networks is required for building any new animal body plan.

Finally, Meyer raises the problem of the origin of epigenetic (i.e., “beyond the gene”) information necessary for constructing animals, a problem that has led many evolutionary biologists to seek a new theory of and mechanism for major evolutionary innovation.

In making his five-fold case against neo-Darwinism, Meyer takes readers on a tour of the peer-reviewed research projects produced by the ID scientific community in recent years.

In Chapter 10, he reviews experimental work by protein scientist Douglas Axe published in Journal of Molecular Biology showing that amino acid sequences that yield functional, stable proteins are as rare as 1 in 1077 sequences.20 Chapter 12 is titled “Complex Adaptations and the Neo-Darwinian Math,” and in it Meyer expounds upon research by biochemist Michael Behe and physicist David Snoke in Protein Science, as well as work from Axe and biologist Ann Gauger in the journal BIO-Complexity, which suggests that multiple coordinated mutations are required to produce many new protein functions.21

Meyer traces the scientific pedigree of these studies back to eminent biologists like Francis Crick and John Maynard Smith, or the distinguished group of mathematicians, engineers, and other scientists who gathered at the Wistar Symposium in 1966. After reviewing some of the basics of population genetics and applying the findings of the latest ID-research, he concludes:

In a real sense, therefore, the neo-Darwinian math is itself showing that the neo- Darwinian mechanism cannot build complex adaptations—including the new information-rich genes and proteins that would have been necessary to build the Cambrian animals.22

Taken together, this research shows that numbers of organisms and generations required for the neo-Darwinian mechanism to produce complex features far exceeds the probabilistic resources realistically available over the history of life on earth.

A Post-Darwinian WorldAt this point in the book, Meyer’s argument pivots. As increasing numbers of evolutionary biologists have acknowledged these problems with the modern synthesis, they have begun to experience what the renowned Cambrian paleontologist Simon Conway Morris has called “Darwin fatigue.” The unresolved problems exposed by the Cambrian explosion have, in Conway Morris’s view, “opened the way to a post-Darwinian world.”23 According to Darwin’s Doubt, we now live in a wild-west period of evolutionary thinking, where multiple models are competing to replace neo-Darwinism.

Meyer tackles many of these “post-Darwinian” models, including self-organization, evolutionary developmental biology, punctuated equilibrium, neo-Lamarckism, natural genetic engineering, neutral evolution, and others. In this regard, Darwin's Doubt offers something entirely novel: it surveys the landscape of these “post-neo-Darwinian evolutionary models,” and shows why they too fail as explanations for the origin of animal body plans and biological complexity.

Conway Morris is hardly the only scientist to admit that the Cambrian explosion remains a challenge to evolutionary biology. In The Cambrian Explosion, Douglas Erwin and James Valentine concede that from their vantage as evolutionary biologists, the Cambrian explosion is currently "unresolved":

The patterns of disparity observed during the Cambrian pose two unresolved questions. First, what evolutionary process produced the gaps between the morphologies of major clades? Second, why have the morphological boundaries of these body plans remained relatively stable over the past half a billion years?24

This is why the journal Science, when recently reviewing Erwin and Valentine's book, stated: “the proximate causes of this body plan revolution remain decidedly murky. The grand puzzle of the Cambrian explosion surely must rank as one of the most important outstanding mysteries in evolutionary biology.”25 Is there a way to solve the mystery of the Cambrian explosion?

A Better Post-Darwinian Model: Intelligent DesignMeyer argues that there is one post-Darwinian model which can explain the mystery of the Cambrian explosion: intelligent design. Using standard scientific methods of historical sciences, rigorous abductive logic, and case studies from the development of technology, Meyer establishes intelligent design as the only known sufficient cause for generating the information and top-down design required building the integrated animal body plans which appear explosively in the Cambrian period. According to Meyer, “our uniform experience of cause and effect shows that intelligent design is the only known cause of the origin of large amounts of functionally specified digital information,”26 which by necessity must have originated in the Cambrian explosion.

Despite strong case Darwin’s Doubt presents for intelligent design, we’re left in a strange position where many leading scientists insist that ID isn’t science, and that neo-Darwinian evolution is as sound as ever. Meyer’s tour de force answers many objections to ID, and cites numerous mainstream scientists and their peer-reviewed publications challenging the core tenets of modern Darwinian theory. According to Meyer:

Rarely has there been such a great disparity between the popular perception of a theory [neo-Darwinism] and its actual standing in the relevant peer-reviewed scientific literature.27

If Meyer is correct, then the fundamentals of neo-Darwinian theory are unsound. With the groundwork for the rejection of Darwinian biology already laid in the peer-reviewed technical literature, how much longer can Darwin defenders maintain the pretense that their theory has no weaknesses? The answer is complicated, and depends on a host of forces, especially the extent to which ID proponents will enjoy academic freedom to promote their views. But for those who simply wish to understand and follow where the evidence leads, Darwin’s Doubt shows there has never been a more exciting time to be a proponent of intelligent design.